Examples with Labeling sc.fiji.labkit.ui.labeling.Labeling used on opensource projects

Example 1 with Labeling

use of sc.fiji.labkit.ui.labeling.Labeling in project labkit-ui by juglab.

the class TrainableSegmentationSegmenter method train.

@Override
public void train(List<Pair<ImgPlus<?>, Labeling>> trainingData) {
    try {
        initFeatureSettings(trainingData);
        List<String> classes = collectLabels(trainingData.stream().map(Pair::getB).collect(Collectors.toList()));
        sc.fiji.labkit.pixel_classification.classification.Segmenter segmenter = new sc.fiji.labkit.pixel_classification.classification.Segmenter(context, classes, featureSettings, new FastRandomForest());
        segmenter.setUseGpu(useGpu);
        Training training = segmenter.training();
        for (Pair<ImgPlus<?>, Labeling> pair : trainingData) trainStack(training, classes, pair.getB(), pair.getA(), segmenter.features());
        training.train();
        this.segmenter = segmenter;
    } catch (RuntimeException e) {
        Throwable cause = e.getCause();
        if (cause instanceof WekaException && cause.getMessage().contains("Not enough training instances"))
            throw new CancellationException("The training requires some labeled regions.");
        throw e;
    }
}

Example 2 with Labeling

use of sc.fiji.labkit.ui.labeling.Labeling in project labkit-ui by juglab.

the class TrainableSegmentationSegmenter method getClassIndices.

private SparseRandomAccessIntType getClassIndices(Labeling labeling, List<String> classes) {
    SparseRandomAccessIntType result = new SparseRandomAccessIntType(labeling, -1);
    Map<Set<Label>, Integer> classIndices = new HashMap<>();
    Function<Set<Label>, Integer> compute = set -> set.stream().mapToInt(label -> classes.indexOf(label.name())).filter(i -> i >= 0).min().orElse(-1);
    Cursor<?> cursor = labeling.sparsityCursor();
    RandomAccess<LabelingType<Label>> randomAccess = labeling.randomAccess();
    RandomAccess<IntType> out = result.randomAccess();
    while (cursor.hasNext()) {
        cursor.fwd();
        randomAccess.setPosition(cursor);
        Set<Label> labels = randomAccess.get();
        if (labels.isEmpty())
            continue;
        Integer classIndex = classIndices.computeIfAbsent(labels, compute);
        out.setPosition(cursor);
        out.get().set(classIndex);
    }
    return result;
}

Example 3 with Labeling

use of sc.fiji.labkit.ui.labeling.Labeling in project labkit-ui by juglab.

the class MultiChannelMovieDemo method testInputImageImageForSegmentation.

@Test
public void testInputImageImageForSegmentation() {
    DatasetInputImage inputImage = inputImage5d();
    SegmentationModel segmentationModel = new DefaultSegmentationModel(new Context(), inputImage);
    SegmentationItem segmenter = segmentationModel.segmenterList().addSegmenter(PixelClassificationPlugin.create());
    Labeling labeling1 = labeling5d();
    segmentationModel.imageLabelingModel().labeling().set(labeling1);
    segmenter.train(Collections.singletonList(new ValuePair<>(inputImage.imageForSegmentation(), labeling1)));
    RandomAccessibleInterval<ShortType> result = segmenter.results(segmentationModel.imageLabelingModel()).segmentation();
    Labeling labeling = labeling5d();
    LoopBuilder.setImages(labeling, result).forEachPixel((l, r) -> {
        if (l.contains("foreground"))
            assertEquals(1, r.get());
        if (l.contains("background"))
            assertEquals(0, r.get());
    });
}

Example 4 with Labeling

use of sc.fiji.labkit.ui.labeling.Labeling in project labkit-ui by juglab.

the class MultiChannelMovieDemo method labeling5d.

private Labeling labeling5d() {
    Labeling labeling = Labeling.createEmpty(Arrays.asList("background", "foreground"), new FinalInterval(20, 10, 10, 20));
    RandomAccess<LabelingType<Label>> ra = labeling.randomAccess();
    ra.setPosition(new long[] { 1, 0, 0, 1 });
    ra.get().add(labeling.getLabel("foreground"));
    ra.setPosition(new long[] { 4, 0, 0, 1 });
    ra.get().add(labeling.getLabel("foreground"));
    ra.setPosition(new long[] { 5, 0, 0, 1 });
    ra.get().add(labeling.getLabel("background"));
    ra.setPosition(new long[] { 0, 0, 0, 1 });
    ra.get().add(labeling.getLabel("background"));
    return labeling;
}

Example 5 with Labeling

use of sc.fiji.labkit.ui.labeling.Labeling in project labkit-ui by juglab.

the class SegmentationUseCaseTest method testMultiChannel.

@Test
public void testMultiChannel() throws InterruptedException {
    Img<UnsignedByteType> img = ArrayImgs.unsignedBytes(new byte[] { -1, 0, -1, 0, -1, -1, 0, 0 }, 2, 2, 2);
    ImgPlus<UnsignedByteType> imgPlus = new ImgPlus<>(img, "Image", new AxisType[] { Axes.X, Axes.Y, Axes.CHANNEL });
    DatasetInputImage inputImage = new DatasetInputImage(imgPlus, BdvShowable.wrap(Views.hyperSlice(img, 2, 0)));
    Labeling labeling = getLabeling();
    SegmentationModel segmentationModel = new DefaultSegmentationModel(new Context(), inputImage);
    ImageLabelingModel imageLabelingModel = segmentationModel.imageLabelingModel();
    imageLabelingModel.labeling().set(labeling);
    SegmentationItem segmenter = segmentationModel.segmenterList().addSegmenter(PixelClassificationPlugin.create());
    segmenter.train(Collections.singletonList(new ValuePair<>(imgPlus, imageLabelingModel.labeling().get())));
    RandomAccessibleInterval<ShortType> result = segmenter.results(imageLabelingModel).segmentation();
    Iterator<ShortType> it = Views.iterable(result).iterator();
    assertEquals(1, it.next().get());
    assertEquals(0, it.next().get());
    assertEquals(0, it.next().get());
    assertEquals(0, it.next().get());
    assertTrue(Intervals.equals(new FinalInterval(2, 2), result));
}